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LOC130000485 ATAC-STARR-seq lymphoblastoid active region 27444 [ Homo sapiens (human) ]

Gene ID: 130000485, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130000485
Gene description
ATAC-STARR-seq lymphoblastoid active region 27444
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence represents an accessible chromatin region that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC130000485 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (61138882..61139021)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (61562601..61562740)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (62051441..62051580)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 10423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27433 Neighboring gene hCG1816373-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27436 Neighboring gene nuclear autoantigenic sperm protein pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27439 Neighboring gene Sharpr-MPRA regulatory region 12445 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:61925128-61925715 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:61925759-61926468 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:61929973-61931172 Neighboring gene clavesin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:61964453-61964975 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:61989140-61989380 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:61989895-61990569 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:61990570-61991243 Neighboring gene meiotic recombination hotspot G Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:62033015-62033646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27441 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19234 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:62075983-62076484 Neighboring gene nucleophosmin 1 pseudogene 6 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:62185690-62186311 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:62186312-62186932 Neighboring gene uncharacterized LOC105375870 Neighboring gene NANOG hESC enhancer GRCh37_chr8:62279520-62280036

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_179931.1 

    Range
    101..240
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    61138882..61139021
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    61562601..61562740
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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